MBMB,BCHM, or CHEM 451A

• This is a team taught course– Blaine Bartholomew: 1st section– Joseph Schmit: 2nd section– Peter Hardwicke: 3rd Section

• Text is Lehninger Principles of Biochemistry 4th edition– Supplementary material found in Genes

VIII which is on reserve at Morris Library

Grading

• Each section is worth 100 points

• The final exam is worth 200 points

• You can drop one of the other exams for a total number of points possible being 400 points

• In my section the points are 30 points for homework and 70 point for my exam

Notes and other helps

• Notes will be posted on web at:http://web.siumed.edu/~bbartholomew/451A_Sec1.html

• Suggested that you print out the lecture outline before class to help you with your in-class note taking

• Don’t forget the suggested readings and problems

And other helpsInstructor

Blaine BartholomewOffice: Neckers Bldg., Rm. 211 Phone: 453-6437 Email: bbartholomew@siumed.edu

Office Hours: Tues and Thurs 2-3 p.m.

Teaching Assistant

Mekonnen DechassaOffice: Neckers Bldg., Rm. 207Phone: 453-1132Email: mekonnen@siu.eduOffice Hours: By appointment only

Science is question driven

How does DNA encode for all the characteristics found

within an organism?

Questions

• How is DNA read by the cell?• What are the distinguishing features of

DNA that accounts for its specificity?• Are there certain chemical or

mechanical properties of DNA that are vital in this process?

• What are those factors (proteins) that “read” DNA and how do they work

Foundations

One must first understand the structural parameters of DNA and its physical properties.

Next it is important to know what are the variations that can be found in nature

Chemical structure and base composition

1. Numbering system of nucleic acids2. Phosphate linkages –

phosphoester bonds3. nucleotide composition4. sugar ring - pucker

Chemical structure and base composition

1. Numbering system of nucleic acidsa. phosphate (alpha, beta,

gamma)

Chemical structure and base composition

1. Numbering system of nucleic acidsa. phosphate (alpha, beta,

gamma) b. base (1,2,3,...)

Chemical structure and base composition

1. Numbering system of nucleic acidsa. phosphate (alpha, beta,

gamma) b. base (1,2,3,...) c. sugar (1', 2', 3', ...)

Chemical structure and base composition

1. Numbering system of nucleic acidsa. phosphate (alpha, beta,

gamma) b. base (1,2,3,...) c. sugar (1', 2', 3', ...)

d. shorthand notation

Chemical structure and base composition

2. Phosphate linkages – phosphoester bonds

a. phosphomonoester bond b. phosphodiester bond

c. phosphotriester bond

Chemical structure and base composition

3. nucleotide a. normal base composition

Chemical structure and base composition

3. nucleotide a. normal base compositionb. modified bases

Modified Bases

Modified Bases

Chemical structure and base composition

3. nucleotide a. normal base compositionb. modified bases c. tautomers

Tautomers

Chemical structure and base composition

4. sugar ring - a. nucleotide vs. nucleosideb. deoxyribose vs. ribose see figure

5-1c. base-catalyzed hydrolysis of RNA

(not DNA)due to 2'-OH of RNA

d. ring pucker: endo vs. exo and C-3' vs C-2'

Nucleotide versus nucleoside

Chemical structure and base composition

4. sugar ring - a. nucleotide vs. nucleosideb. deoxyribose vs. ribose see figure

5-1c. base-catalyzed hydrolysis of RNA

(not DNA)due to 2'-OH of RNA

d. ring pucker: endo vs. exo and C-3' vs C-2'

Chemical structure and base composition

4. sugar ring - a. nucleotide vs. nucleosideb. deoxyribose vs. ribose see figure

5-1c. base-catalyzed hydrolysis of RNA

(not DNA)due to 2'-OH of RNA

d. ring pucker: endo vs. exo and C-3' vs C-2'

Alkaline Hydrolysis of RNA

Chemical structure and base composition

4. sugar ring - a. nucleotide vs. nucleosideb. deoxyribose vs. ribose see figure

5-1c. base-catalyzed hydrolysis of RNA

(not DNA)due to 2'-OH of RNA

d. ring pucker: endo vs. exo and C-3' vs C-2'

Ring Pucker

Double Helical Structures

1. Watson Crick Structure: B-DNA a. antiparallel orientation, 3' vs 5' ends b. base pairing interactions

i. always a purine-pyrimidine (steric constraints)

ii. tautomeric forms of bases

c. double helical parameters d. real DNA deviates from the ideal B-DNA form

Double Helical Structures

1. Watson Crick Structure: B-DNA c. double helical parameters

i. helical sense: right vs leftii. major vs minor grooveiii. base pairs per helical turniv. helix rise per base pair or helical pitch

distance from one step to the nextv. helical twist: angle between two adjacent base pairs

=360 deg/base pairs per turnvi. base tilt: slant of the step, not completely planarvii. glycosidic conformation: anti vs syn - figure 29-8viii. sugar ring pucker: 4 out of 5 ring atoms are nearly planar

the 5th atom is usually the C-2 or C-3 atom endo vs exo

Double Helical Structures

1. Watson Crick Structure: B-DNA d. real DNA deviates from the ideal B-DNA form

i. local deviations are commonii. some DNA is naturally bentiii. deviations are sequence dependent

Double Helical Structures

1. Watson Crick Structure: B-DNA d. real DNA deviates from the ideal B-DNA form

i. local deviations are commonii. some DNA is naturally bentiii. deviations are sequence dependent

Double Helical Structures

2. A-DNAa. wider and flatter than B-DNAi. very shallow minor grooveii. deeper major grooveb. tilt is 20 deg (most tilted)c. dried out DNA, 75% vs 92% humidityd. flat ribbon wound around a 6 angstrom holee. found in spores because of close packaging and RNA-RNA/RNA-DNA hybrids assume an A-DNA like structure

Double Helical Structures

3. Z-DNA a. Characteristics of

i. occurs in alternating purine-pyrimidine tracts

ii. favored in high salt;helps eliminate electrostatic repulsion of phosphate groups (8 vs 12 angstrom distance)

iii. methylation of deoxycytidine helps formation of Z-DNA

iv. phosphate backbone forms a zig-zag conformation

Double Helical Structures

3. Z-DNAb. double helical parameters

i. syn vs. anti conformationpurines flip to assume syn

ii. helical sense is left handed iii. deep minor groove, no major groove

c. biological role of Z-DNAi. unclear at this pointii. anti Z-DNA antibody detection, artifactualiii. methylation proved to be less artificial

Double Helical Structures

3. Z-DNA figure 29-3 a & bb. double helical parameters

i. syn vs. anti conformationpurines flip to assume syn

ii. helical sense is left handed iii. deep minor groove, no major groove

c. biological role of Z-DNAi. unclear at this pointii. anti Z-DNA antibody detection, artifactualiii. methylation proved to be less artificial

Double Helical Structures

4. Unusual DNA structuresa. palindrome vs. mirror repeat

i. example - placement of invert repeats

ii. hairpiniii. cruciform

b. Hoogsteen base pairingi. triplex formation - figure a and bii. G tetraplex - found at telomeres

c. Triple helix

Double Helical Structures

4. Unusual DNA structuresa. palindrome vs. mirror repeat

i. example - placement of invert repeats

ii. hairpiniii. cruciform

b. Hoogsteen base pairingi. triplex formationii. G tetraplex - found at telomeres

c. Triple helix

Double Helical Structures

4. Unusual DNA structuresa. palindrome vs. mirror repeat

i. example - placement of invert repeats

ii. hairpiniii. cruciform

b. Hoogsteen base pairingi. triplex formation - figure a and bii. G tetraplex - found at telomeres

c. Triple helix

Forces that help to form the DNA double helix

1. Rigid phosphate backbone2. Stacking interactions - electronic interactions

between planar bases3. Hydrophobic interactions - highly negative

phosphate backbone vs. nonpolar bases4. Hydrogen bonding is not the most energetically

significant componentnote: maintenance of distance from the two

phosphate backbone requires Pur-Pyr5. Ionic interactions - salt stabilizes the duplex form

of DNAshielding of phosphate backbone

Denaturation and Renaturation

1. Tm: (melting temperature) temperature at which half of the DNA is melted

Marmur-Doty equation for Tm correlated to G+C percent and salt

Tm=41.1 XG+C + 16.6 log[Na+] + 81.5

2. Denaturation is a cooperative process -caused by: heat, change in pH, organic

solvents (urea, formamide)3. Hyperchromic shift - increase of absorbance of

DNA when it goes from being double- to single- stranded

40% increase in absorbance 4. Annealing:Hybridization